MolNFT v1 · #149429 · protein + DNA
The crystal structure of the POL2 catalytic domain of DNA polymerase epsilon carrying a P301R substitution.
6G0A · DNA polymerase epsilon catalytic subunit a: “The crystal structure of the POL2 catalytic domain of DNA polymerase epsilon carrying a P301R substitution.”. X-ray diffraction, 3 ligands (DTP, CA, FE), 12 pockets (best druggability…
- PDB
- 6G0A
- Type
- protein + DNA
- Length
- 1,130 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase epsilon catalytic subunit a; DNA…
- EC
- 2.7.7.7
- UniProt
- P21951
- Ligands
- DTP, CA, FE
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase epsilon catalytic subunit a (EC 2.7.7.7) | protein | 1104 | 42% helix, 22% strand | P21951 |
| P | DNA (5'-D(P*TP*AP*AP*CP*CP*GP*CP*GP*TP*TP*DC)-3') | dna | 11 | — | — |
| T | DNA (5'-D(P*TP*CP*TP*TP*GP*AP*AP*CP*GP*CP*GP*GP*TP*TP*A)- 3') | dna | 15 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, P, T
- CA · Calcium ion · metal · 2 copies · chains A
- FE · Fe (III) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 780 | 0.76 | 0.80 | 61 | DTP, CA |
| 2 | 665 | 0.71 | 0.78 | 59 | CA |
| 3 | 800 | 0.71 | 0.77 | 62 | empty |
| 4 | 357 | 0.70 | 0.83 | 34 | empty |
| 5 | 121 | 0.42 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1285 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–P · 852 Ų buried · 22 hydrogen bonds · protein-nucleic
- P–T · 492 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6G0A · The crystal structure of the Pol2 catalytic domain of DNA polymerase epsilon carrying a… · the same entry in another collection · chain A against A, TM-score 1.00
- P21951 · AlphaFold monomer V2.0 prediction for DNA polymerase epsilon catalytic subunit a (P21951) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P21951
- Elsewhere: RCSB PDB 6G0A · PDBe 6G0A · UniProt P21951
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